ODE add-on to CellNOptR


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Documentation for package ‘CNORode’ version 1.30.0

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cnodata A cnodata from CellNoptR
cnolist A cnolist from CellNoptR
cnolistCNORodeExample A cnolist from CellNoptR
CNORode Logic based ODE extension for CellNOptR
createLBodeContPars Create a list with ODE parameter information needed to perform parameter estimation
crossvalidateODE k-fold crossvalidation for ODE models.
defaultParametersGA Create default options to perform parameter estimation with a genetic algorithm.
defaultParametersSSm Create default options to perform parameter estimation with scatter search meta-heuristic.
getLBodeContObjFunction Returns the objective function to perform parameter estimation.
getLBodeDataSim Simulate value signals a CNO list With Logic-Based ODEs.
getLBodeMINLPObjFunction Get the objective function to evaluate the fitness of a given model structure and set of parameters.
getLBodeModelSim Simulate the logic-based ODE model
getLBodeSimFunction Get a function to simulate a logic based ODE model.
getStates Find which species in the model are states.
incidence2Adjacency Convert an incidence matrix into an adjacency matrix.
indices Indices that relate cnolist to model
minlpLBodeSSm Search for the best combination of continuous parameters and logic gates.
model A model from CellNoptR
parEstimationLBode Perform parameter estimation using a genetic algorithm (package genalg) or ssm (if package essm available).
parEstimationLBodeGA Perform parameter estimation using a genetic algorithm (package genalg).
parEstimationLBodeSSm Perform parameter estimation using essR.
pknmodel A pknmodel from CellNoptR
plotLBodeFitness Plot data against simulated values.
plotLBodeModelSim Simulate the model and plot the obtained with the different experimental conditions.
runCNORode runCNORode
simdata2cnolist converts output of getLBodeModelSim to cnolist
simulate Simulate value signals a CNO list With Logic-Based ODEs.